Mercurial > repos > jpayne > bioproject2srr

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planemo upload commit 27af5cba48986d508a67a5024a3bd35dd47bee15-dirty
author jpayne
date Mon, 08 Dec 2025 20:18:03 +0000
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79fa4330f2c9 planemo upload commit 27af5cba48986d508a67a5024a3bd35dd47bee15-dirty
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1 import pytest
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2
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3 from bio2srr import *
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4
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5
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6 def test_element_tree_xpath():
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7 from xml.etree import ElementTree as xml
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8 root = xml.fromstring(biosample_example)
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9 assert root.find(".//Id[@db='BioSample']") is not None
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10
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11 def test_flatten_biosample_xml():
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12 d = flatten_biosample_xml(biosample_example)
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13 assert d['biosample_accession'] == 'SAMN17131268'
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14 assert d['organism'] == 'Campylobacter jejuni'
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15 assert d['isolate'] == 'CFSAN091032'
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16
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17 def test_flatten_runs():
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18 d = list(flatten_runs(runs_example))
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19 assert len(d) == 2
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20
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21 def test_header_sort_override_consistency():
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22 import random
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23 L = ["C", "B", "A", "taxid", "bioproject"]
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24 L.sort(key=hso)
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25 # assert L[0] == "bioproject"
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26 A = L.copy()
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27 assert A == L
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28 R = []
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29 for _ in range(100):
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30 random.shuffle(A)
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31 A.sort(key=hso)
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32 R.append(A == L)
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33 assert all(R)
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34
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35 def test_hso_override():
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36 assert header_sort_override("bioproject", "taxid") < 0
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37 assert header_sort_override("taxid", "bioproject") > 0
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38 assert header_sort_override("taxid", "taxid") == 0
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39
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40 def test_hso_regular():
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41 assert header_sort_override("A", "B") < 0
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42 assert header_sort_override("B", "A") > 0